EPFL course by Vincent Gardeux
06.04.2022 - Prague
In recent years, single-cell transcriptomics has become a widely used technology to study heterogeneous and dynamic biological systems. A large number of new tools and approaches have been developed for analyzing this new type of data.
The goal of this hands-on session is to provide theoretical and practical knowledge in the basic analysis of single-cell RNA-seq datasets.
This course covers the standard analysis of a single-cell RNA-seq dataset using the Seurat pipeline. It follows to some extent the "standard tutorial from Seurat", which we encourage the readers to consult when they want to dive more into single-cell data analyis.
In this course, we will use an example data set consisting of 7,000 cells from the "Fly Cell Atlas" repository. These cells all come from the Body part, which was dissociated as a whole and sequenced using 10x Genomics technology over 10 batches, mixing males and females.
This set of 7,000 cells was carefully selected/filtered from the original Body dataset that consists of 96,926 cells. They belong to a certain number of differently annotated cell types.
06.04.2022 - Prague
This course will take place on-site, at the ENHPATHY event IV meeting, in Prague.
After a short introduction to single-cell genomics, and more particularly single-cell transcriptomics, we will go to and R exercise together.
For the full schedule of the ENHPATHY meeting, please go to: Schedule
At the end of this session, the participants should be able to:
- have a global knowledge of what is single-cell genomics, and in particular single-cell transcriptomics,
- have a good understanding of the generic analysis pipeline for scRNA-seq,
- repeat the same type of analysis achieved during the mini-project,
- present the mini-project and more globally disseminate their experience to the members of their group.
Pre-requisites - background knowledge
- Intermediate/advanced usage of R is a plus
Pre-requisites - material & software
- The participants must use a laptop with install permissions (admin). R and Rstudio should be installed on their machine. Two packages need to be installed, with their dependencies:
install.packages("Seurat")
install.packages("data.table")
- Vincent Gardeux, Senior Scientist, EPFL, Lausanne, 🇨🇭 Switzerland
Additional information
For more information, please contact vincent.gardeux@epfl.ch.